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<h1 class="toc">Everything</h1>
<hr />
  <h2 class="toc">All Classes</h2>
  <div class="private">
    <a target="mainFrame" href="dadi.Plotting._sfsTickLocator-class.html"
     >dadi.Plotting._sfsTickLocator</a><br />  </div>
    <a target="mainFrame" href="dadi.RunInParallel.Statement-class.html"
     >dadi.RunInParallel.Statement</a><br />    <a target="mainFrame" href="dadi.Spectrum_mod.Spectrum-class.html"
     >dadi.Spectrum_mod.Spectrum</a><br />    <a target="mainFrame" href="matplotlib.ticker.TickHelper.DummyAxis-class.html"
     >matplotlib.ticker.TickHelper.DummyAxis</a><br />  <h2 class="toc">All Functions</h2>
    <a target="mainFrame" href="dadi.Demographics1D-module.html#bottlegrowth"
     >dadi.Demographics1D.bottlegrowth</a><br />    <a target="mainFrame" href="dadi.Demographics1D-module.html#growth"
     >dadi.Demographics1D.growth</a><br />    <a target="mainFrame" href="dadi.Demographics1D-module.html#snm"
     >dadi.Demographics1D.snm</a><br />    <a target="mainFrame" href="dadi.Demographics1D-module.html#three_epoch"
     >dadi.Demographics1D.three_epoch</a><br />    <a target="mainFrame" href="dadi.Demographics1D-module.html#two_epoch"
     >dadi.Demographics1D.two_epoch</a><br />    <a target="mainFrame" href="dadi.Demographics2D-module.html#IM"
     >dadi.Demographics2D.IM</a><br />    <a target="mainFrame" href="dadi.Demographics2D-module.html#IM_mscore"
     >dadi.Demographics2D.IM_mscore</a><br />    <a target="mainFrame" href="dadi.Demographics2D-module.html#IM_pre"
     >dadi.Demographics2D.IM_pre</a><br />    <a target="mainFrame" href="dadi.Demographics2D-module.html#IM_pre_mscore"
     >dadi.Demographics2D.IM_pre_mscore</a><br />    <a target="mainFrame" href="dadi.Demographics2D-module.html#bottlegrowth"
     >dadi.Demographics2D.bottlegrowth</a><br />    <a target="mainFrame" href="dadi.Demographics2D-module.html#bottlegrowth_split"
     >dadi.Demographics2D.bottlegrowth_split</a><br />    <a target="mainFrame" href="dadi.Demographics2D-module.html#bottlegrowth_split_mig"
     >dadi.Demographics2D.bottlegrowth_split_mig</a><br />    <a target="mainFrame" href="dadi.Demographics2D-module.html#snm"
     >dadi.Demographics2D.snm</a><br />    <a target="mainFrame" href="dadi.Demographics2D-module.html#split_mig"
     >dadi.Demographics2D.split_mig</a><br />    <a target="mainFrame" href="dadi.Demographics2D-module.html#split_mig_mscore"
     >dadi.Demographics2D.split_mig_mscore</a><br />    <a target="mainFrame" href="dadi.Hessian-module.html#hessian"
     >dadi.Hessian.hessian</a><br />    <a target="mainFrame" href="dadi.Hessian-module.html#hessian_elem"
     >dadi.Hessian.hessian_elem</a><br />    <a target="mainFrame" href="dadi.Inference-module.html#Anscombe_Poisson_residual"
     >dadi.Inference.Anscombe_Poisson_residual</a><br />  <div class="private">
    <a target="mainFrame" href="dadi.Inference-module.html#_object_func"
     >dadi.Inference._object_func</a><br />  </div>
  <div class="private">
    <a target="mainFrame" href="dadi.Inference-module.html#_object_func_log"
     >dadi.Inference._object_func_log</a><br />  </div>
  <div class="private">
    <a target="mainFrame" href="dadi.Inference-module.html#_project_params_down"
     >dadi.Inference._project_params_down</a><br />  </div>
  <div class="private">
    <a target="mainFrame" href="dadi.Inference-module.html#_project_params_up"
     >dadi.Inference._project_params_up</a><br />  </div>
    <a target="mainFrame" href="dadi.Inference-module.html#linear_Poisson_residual"
     >dadi.Inference.linear_Poisson_residual</a><br />    <a target="mainFrame" href="dadi.Inference-module.html#ll"
     >dadi.Inference.ll</a><br />    <a target="mainFrame" href="dadi.Inference-module.html#ll_multinom"
     >dadi.Inference.ll_multinom</a><br />    <a target="mainFrame" href="dadi.Inference-module.html#ll_multinom_per_bin"
     >dadi.Inference.ll_multinom_per_bin</a><br />    <a target="mainFrame" href="dadi.Inference-module.html#ll_per_bin"
     >dadi.Inference.ll_per_bin</a><br />    <a target="mainFrame" href="dadi.Inference-module.html#minus_ll"
     >dadi.Inference.minus_ll</a><br />    <a target="mainFrame" href="dadi.Inference-module.html#minus_ll_multinom"
     >dadi.Inference.minus_ll_multinom</a><br />    <a target="mainFrame" href="dadi.Inference-module.html#optimal_sfs_scaling"
     >dadi.Inference.optimal_sfs_scaling</a><br />    <a target="mainFrame" href="dadi.Inference-module.html#optimally_scaled_sfs"
     >dadi.Inference.optimally_scaled_sfs</a><br />    <a target="mainFrame" href="dadi.Inference-module.html#optimize"
     >dadi.Inference.optimize</a><br />    <a target="mainFrame" href="dadi.Inference-module.html#optimize_grid"
     >dadi.Inference.optimize_grid</a><br />    <a target="mainFrame" href="dadi.Inference-module.html#optimize_lbfgsb"
     >dadi.Inference.optimize_lbfgsb</a><br />    <a target="mainFrame" href="dadi.Inference-module.html#optimize_log"
     >dadi.Inference.optimize_log</a><br />    <a target="mainFrame" href="dadi.Inference-module.html#optimize_log_fmin"
     >dadi.Inference.optimize_log_fmin</a><br />    <a target="mainFrame" href="dadi.Inference-module.html#optimize_log_lbfgsb"
     >dadi.Inference.optimize_log_lbfgsb</a><br />  <div class="private">
    <a target="mainFrame" href="dadi.Integration-module.html#_Mfunc1D"
     >dadi.Integration._Mfunc1D</a><br />  </div>
  <div class="private">
    <a target="mainFrame" href="dadi.Integration-module.html#_Mfunc1D_X"
     >dadi.Integration._Mfunc1D_X</a><br />  </div>
  <div class="private">
    <a target="mainFrame" href="dadi.Integration-module.html#_Mfunc2D"
     >dadi.Integration._Mfunc2D</a><br />  </div>
  <div class="private">
    <a target="mainFrame" href="dadi.Integration-module.html#_Mfunc3D"
     >dadi.Integration._Mfunc3D</a><br />  </div>
  <div class="private">
    <a target="mainFrame" href="dadi.Integration-module.html#_Vfunc"
     >dadi.Integration._Vfunc</a><br />  </div>
  <div class="private">
    <a target="mainFrame" href="dadi.Integration-module.html#_Vfunc_X"
     >dadi.Integration._Vfunc_X</a><br />  </div>
  <div class="private">
    <a target="mainFrame" href="dadi.Integration-module.html#_compute_delj"
     >dadi.Integration._compute_delj</a><br />  </div>
  <div class="private">
    <a target="mainFrame" href="dadi.Integration-module.html#_compute_dfactor"
     >dadi.Integration._compute_dfactor</a><br />  </div>
  <div class="private">
    <a target="mainFrame" href="dadi.Integration-module.html#_compute_dt"
     >dadi.Integration._compute_dt</a><br />  </div>
  <div class="private">
    <a target="mainFrame" href="dadi.Integration-module.html#_inject_mutations_1D"
     >dadi.Integration._inject_mutations_1D</a><br />  </div>
  <div class="private">
    <a target="mainFrame" href="dadi.Integration-module.html#_inject_mutations_1D_X"
     >dadi.Integration._inject_mutations_1D_X</a><br />  </div>
  <div class="private">
    <a target="mainFrame" href="dadi.Integration-module.html#_inject_mutations_2D"
     >dadi.Integration._inject_mutations_2D</a><br />  </div>
  <div class="private">
    <a target="mainFrame" href="dadi.Integration-module.html#_inject_mutations_3D"
     >dadi.Integration._inject_mutations_3D</a><br />  </div>
  <div class="private">
    <a target="mainFrame" href="dadi.Integration-module.html#_one_pop_const_params"
     >dadi.Integration._one_pop_const_params</a><br />  </div>
  <div class="private">
    <a target="mainFrame" href="dadi.Integration-module.html#_one_pop_const_params_X"
     >dadi.Integration._one_pop_const_params_X</a><br />  </div>
  <div class="private">
    <a target="mainFrame" href="dadi.Integration-module.html#_three_pops_const_params"
     >dadi.Integration._three_pops_const_params</a><br />  </div>
  <div class="private">
    <a target="mainFrame" href="dadi.Integration-module.html#_two_pops_const_params"
     >dadi.Integration._two_pops_const_params</a><br />  </div>
    <a target="mainFrame" href="dadi.Integration-module.html#one_pop"
     >dadi.Integration.one_pop</a><br />    <a target="mainFrame" href="dadi.Integration-module.html#one_pop_X"
     >dadi.Integration.one_pop_X</a><br />    <a target="mainFrame" href="dadi.Integration-module.html#set_timescale_factor"
     >dadi.Integration.set_timescale_factor</a><br />    <a target="mainFrame" href="dadi.Integration-module.html#three_pops"
     >dadi.Integration.three_pops</a><br />    <a target="mainFrame" href="dadi.Integration-module.html#two_pops"
     >dadi.Integration.two_pops</a><br />    <a target="mainFrame" href="dadi.Misc-module.html#delayed_flush"
     >dadi.Misc.delayed_flush</a><br />    <a target="mainFrame" href="dadi.Misc-module.html#ensure_1arg_func"
     >dadi.Misc.ensure_1arg_func</a><br />    <a target="mainFrame" href="dadi.Misc-module.html#make_data_dict"
     >dadi.Misc.make_data_dict</a><br />    <a target="mainFrame" href="dadi.Misc-module.html#make_fux_table"
     >dadi.Misc.make_fux_table</a><br />    <a target="mainFrame" href="dadi.Misc-module.html#ms_command"
     >dadi.Misc.ms_command</a><br />    <a target="mainFrame" href="dadi.Misc-module.html#perturb_params"
     >dadi.Misc.perturb_params</a><br />    <a target="mainFrame" href="dadi.Misc-module.html#total_instantaneous_rate"
     >dadi.Misc.total_instantaneous_rate</a><br />    <a target="mainFrame" href="dadi.Misc-module.html#tri_freq_dict_to_array"
     >dadi.Misc.tri_freq_dict_to_array</a><br />    <a target="mainFrame" href="dadi.Misc-module.html#zero_diag"
     >dadi.Misc.zero_diag</a><br />  <div class="private">
    <a target="mainFrame" href="dadi.Numerics-module.html#_cached_projection"
     >dadi.Numerics._cached_projection</a><br />  </div>
  <div class="private">
    <a target="mainFrame" href="dadi.Numerics-module.html#_lncomb"
     >dadi.Numerics._lncomb</a><br />  </div>
    <a target="mainFrame" href="dadi.Numerics-module.html#array_from_file"
     >dadi.Numerics.array_from_file</a><br />    <a target="mainFrame" href="dadi.Numerics-module.html#array_to_file"
     >dadi.Numerics.array_to_file</a><br />    <a target="mainFrame" href="dadi.Numerics-module.html#cubic_extrap"
     >dadi.Numerics.cubic_extrap</a><br />    <a target="mainFrame" href="dadi.Numerics-module.html#end_point_first_derivs"
     >dadi.Numerics.end_point_first_derivs</a><br />    <a target="mainFrame" href="dadi.Numerics-module.html#estimate_best_exp_grid_crwd"
     >dadi.Numerics.estimate_best_exp_grid_crwd</a><br />    <a target="mainFrame" href="dadi.Numerics-module.html#exponential_grid"
     >dadi.Numerics.exponential_grid</a><br />    <a target="mainFrame" href="dadi.Numerics-module.html#intersect_masks"
     >dadi.Numerics.intersect_masks</a><br />    <a target="mainFrame" href="dadi.Numerics-module.html#linear_extrap"
     >dadi.Numerics.linear_extrap</a><br />    <a target="mainFrame" href="dadi.Numerics-module.html#make_extrap_func"
     >dadi.Numerics.make_extrap_func</a><br />    <a target="mainFrame" href="dadi.Numerics-module.html#make_extrap_log_func"
     >dadi.Numerics.make_extrap_log_func</a><br />    <a target="mainFrame" href="dadi.Numerics-module.html#quadratic_extrap"
     >dadi.Numerics.quadratic_extrap</a><br />    <a target="mainFrame" href="dadi.Numerics-module.html#quadratic_grid"
     >dadi.Numerics.quadratic_grid</a><br />    <a target="mainFrame" href="dadi.Numerics-module.html#quartic_extrap"
     >dadi.Numerics.quartic_extrap</a><br />    <a target="mainFrame" href="dadi.Numerics-module.html#quintic_extrap"
     >dadi.Numerics.quintic_extrap</a><br />    <a target="mainFrame" href="dadi.Numerics-module.html#reverse_array"
     >dadi.Numerics.reverse_array</a><br />    <a target="mainFrame" href="dadi.Numerics-module.html#trapz"
     >dadi.Numerics.trapz</a><br />  <div class="private">
    <a target="mainFrame" href="dadi.PhiManip-module.html#_admixture_intermediates"
     >dadi.PhiManip._admixture_intermediates</a><br />  </div>
  <div class="private">
    <a target="mainFrame" href="dadi.PhiManip-module.html#_three_pop_admixture_intermediates"
     >dadi.PhiManip._three_pop_admixture_intermediates</a><br />  </div>
  <div class="private">
    <a target="mainFrame" href="dadi.PhiManip-module.html#_two_pop_admixture_intermediates"
     >dadi.PhiManip._two_pop_admixture_intermediates</a><br />  </div>
    <a target="mainFrame" href="dadi.PhiManip-module.html#phi_1D"
     >dadi.PhiManip.phi_1D</a><br />    <a target="mainFrame" href="dadi.PhiManip-module.html#phi_1D_X"
     >dadi.PhiManip.phi_1D_X</a><br />    <a target="mainFrame" href="dadi.PhiManip-module.html#phi_1D_genic"
     >dadi.PhiManip.phi_1D_genic</a><br />    <a target="mainFrame" href="dadi.PhiManip-module.html#phi_1D_snm"
     >dadi.PhiManip.phi_1D_snm</a><br />    <a target="mainFrame" href="dadi.PhiManip-module.html#phi_1D_to_2D"
     >dadi.PhiManip.phi_1D_to_2D</a><br />    <a target="mainFrame" href="dadi.PhiManip-module.html#phi_2D_admix_1_into_2"
     >dadi.PhiManip.phi_2D_admix_1_into_2</a><br />    <a target="mainFrame" href="dadi.PhiManip-module.html#phi_2D_admix_2_into_1"
     >dadi.PhiManip.phi_2D_admix_2_into_1</a><br />    <a target="mainFrame" href="dadi.PhiManip-module.html#phi_2D_to_3D_admix"
     >dadi.PhiManip.phi_2D_to_3D_admix</a><br />    <a target="mainFrame" href="dadi.PhiManip-module.html#phi_2D_to_3D_split_1"
     >dadi.PhiManip.phi_2D_to_3D_split_1</a><br />    <a target="mainFrame" href="dadi.PhiManip-module.html#phi_2D_to_3D_split_2"
     >dadi.PhiManip.phi_2D_to_3D_split_2</a><br />    <a target="mainFrame" href="dadi.PhiManip-module.html#phi_3D_admix_1_and_2_into_3"
     >dadi.PhiManip.phi_3D_admix_1_and_2_into_3</a><br />    <a target="mainFrame" href="dadi.PhiManip-module.html#phi_3D_admix_1_and_3_into_2"
     >dadi.PhiManip.phi_3D_admix_1_and_3_into_2</a><br />    <a target="mainFrame" href="dadi.PhiManip-module.html#phi_3D_admix_2_and_3_into_1"
     >dadi.PhiManip.phi_3D_admix_2_and_3_into_1</a><br />    <a target="mainFrame" href="dadi.PhiManip-module.html#remove_pop"
     >dadi.PhiManip.remove_pop</a><br />    <a target="mainFrame" href="dadi.Plotting-module.html#plot_1d_comp_Poisson"
     >dadi.Plotting.plot_1d_comp_Poisson</a><br />    <a target="mainFrame" href="dadi.Plotting-module.html#plot_1d_comp_multinom"
     >dadi.Plotting.plot_1d_comp_multinom</a><br />    <a target="mainFrame" href="dadi.Plotting-module.html#plot_1d_fs"
     >dadi.Plotting.plot_1d_fs</a><br />    <a target="mainFrame" href="dadi.Plotting-module.html#plot_2d_comp_Poisson"
     >dadi.Plotting.plot_2d_comp_Poisson</a><br />    <a target="mainFrame" href="dadi.Plotting-module.html#plot_2d_comp_multinom"
     >dadi.Plotting.plot_2d_comp_multinom</a><br />    <a target="mainFrame" href="dadi.Plotting-module.html#plot_2d_resid"
     >dadi.Plotting.plot_2d_resid</a><br />    <a target="mainFrame" href="dadi.Plotting-module.html#plot_3d_comp_Poisson"
     >dadi.Plotting.plot_3d_comp_Poisson</a><br />    <a target="mainFrame" href="dadi.Plotting-module.html#plot_3d_comp_multinom"
     >dadi.Plotting.plot_3d_comp_multinom</a><br />    <a target="mainFrame" href="dadi.Plotting-module.html#plot_3d_spectrum"
     >dadi.Plotting.plot_3d_spectrum</a><br />    <a target="mainFrame" href="dadi.Plotting-module.html#plot_3d_spectrum_mayavi"
     >dadi.Plotting.plot_3d_spectrum_mayavi</a><br />    <a target="mainFrame" href="dadi.Plotting-module.html#plot_single_2d_sfs"
     >dadi.Plotting.plot_single_2d_sfs</a><br />    <a target="mainFrame" href="dadi.RunInParallel-module.html#eval_func_over_list"
     >dadi.RunInParallel.eval_func_over_list</a><br />    <a target="mainFrame" href="dadi.RunInParallel-module.html#make_parallel_gradient_func"
     >dadi.RunInParallel.make_parallel_gradient_func</a><br />    <a target="mainFrame" href="dadi.RunInParallel-module.html#statement_to_all_workers"
     >dadi.RunInParallel.statement_to_all_workers</a><br />    <a target="mainFrame" href="dadi.RunInParallel-module.html#stop_workers"
     >dadi.RunInParallel.stop_workers</a><br />    <a target="mainFrame" href="None"
     >dadi.Spectrum_mod.Spectrum_pickler</a><br />    <a target="mainFrame" href="None"
     >dadi.Spectrum_mod.Spectrum_unpickler</a><br />  <h2 class="toc">All Variables</h2>
    <a target="mainFrame" href="dadi.Demographics1D-module.html#__package__"
     >dadi.Demographics1D.__package__</a><br />    <a target="mainFrame" href="dadi.Demographics2D-module.html#__package__"
     >dadi.Demographics2D.__package__</a><br />    <a target="mainFrame" href="dadi.Hessian-module.html#__package__"
     >dadi.Hessian.__package__</a><br />    <a target="mainFrame" href="dadi.Hessian-module.html#logger"
     >dadi.Hessian.logger</a><br />    <a target="mainFrame" href="dadi.Inference-module.html#__package__"
     >dadi.Inference.__package__</a><br />  <div class="private">
    <a target="mainFrame" href="dadi.Inference-module.html#_counter"
     >dadi.Inference._counter</a><br />  </div>
  <div class="private">
    <a target="mainFrame" href="dadi.Inference-module.html#_out_of_bounds_val"
     >dadi.Inference._out_of_bounds_val</a><br />  </div>
  <div class="private">
    <a target="mainFrame" href="dadi.Inference-module.html#_theta_store"
     >dadi.Inference._theta_store</a><br />  </div>
    <a target="mainFrame" href="dadi.Inference-module.html#index_exp"
     >dadi.Inference.index_exp</a><br />    <a target="mainFrame" href="dadi.Inference-module.html#logger"
     >dadi.Inference.logger</a><br />    <a target="mainFrame" href="dadi.Integration-module.html#__package__"
     >dadi.Integration.__package__</a><br />    <a target="mainFrame" href="dadi.Integration-module.html#logger"
     >dadi.Integration.logger</a><br />    <a target="mainFrame" href="dadi.Integration-module.html#old_timescale_factor"
     >dadi.Integration.old_timescale_factor</a><br />    <a target="mainFrame" href="dadi.Integration-module.html#timescale_factor"
     >dadi.Integration.timescale_factor</a><br />    <a target="mainFrame" href="dadi.Integration-module.html#use_delj_trick"
     >dadi.Integration.use_delj_trick</a><br />    <a target="mainFrame" href="dadi.Integration-module.html#use_old_timestep"
     >dadi.Integration.use_old_timestep</a><br />    <a target="mainFrame" href="dadi.Misc-module.html#__package__"
     >dadi.Misc.__package__</a><br />  <div class="private">
    <a target="mainFrame" href="dadi.Misc-module.html#__times_last_flushed"
     >dadi.Misc.__times_last_flushed</a><br />  </div>
    <a target="mainFrame" href="dadi.Misc-module.html#code"
     >dadi.Misc.code</a><br />    <a target="mainFrame" href="dadi.Numerics-module.html#__package__"
     >dadi.Numerics.__package__</a><br />  <div class="private">
    <a target="mainFrame" href="dadi.Numerics-module.html#_projection_cache"
     >dadi.Numerics._projection_cache</a><br />  </div>
    <a target="mainFrame" href="dadi.Numerics-module.html#logger"
     >dadi.Numerics.logger</a><br />    <a target="mainFrame" href="dadi.PhiManip-module.html#__package__"
     >dadi.PhiManip.__package__</a><br />    <a target="mainFrame" href="dadi.Plotting-module.html#__package__"
     >dadi.Plotting.__package__</a><br />  <div class="private">
    <a target="mainFrame" href="dadi.Plotting-module.html#_ctf"
     >dadi.Plotting._ctf</a><br />  </div>
  <div class="private">
    <a target="mainFrame" href="dadi.Plotting-module.html#_extend_mapping"
     >dadi.Plotting._extend_mapping</a><br />  </div>
    <a target="mainFrame" href="dadi.RunInParallel-module.html#HAVE_PYPAR"
     >dadi.RunInParallel.HAVE_PYPAR</a><br />    <a target="mainFrame" href="dadi.RunInParallel-module.html#__package__"
     >dadi.RunInParallel.__package__</a><br />    <a target="mainFrame" href="dadi.RunInParallel-module.html#currdir"
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